以親緣基因體學探討菲律賓秋海棠組之生物地理學及種化

Abstract

地理上位處歐亞板塊與菲律賓海板塊交界，同時也位於亞洲及澳洲生物區系地理交界處的菲律賓，不論是地質歷史或是生物地理模式都是整個馬來西亞地區最複雜的地方，同時也造就具高度多樣性、參雜複雜演化歷史的物種，然而目前對於菲律賓生物地理學的研究多偏向動物生物地理，對於植物生物地理探討卻未受到等量的關注。本論文研究主要分布在菲律賓群島的秋海棠屬菲律賓秋海棠組 (Begonia sect. Baryandra)，利用次世代定序技術以基因體略讀組裝質體基因體，並以標靶基因獲取取得大量核基因資料，重建高解析度的物種親緣關係，並藉由分子定年、祖先區域重建及檢測種內基因流動事件，揭示物種散佈歷史及可能種化機制。結果顯示，菲律賓秋海棠組於中新世晚期透過西方的長距離傳播事件，首先進入群島中分布最西邊的巴拉望島，隨後的板塊運動、更新世氣候波動等都與該類群植物拓殖其他島嶼相關，並促使植物進一步分化。而除地質、氣候等因素，親緣關係網絡分析顯示，同倍體雜交種化、葉綠體捕獲、多物種雜交等，均造成質體基因樹與核基因樹間的高度不一致，顯示菲律賓秋海棠組內植物間生殖隔離不顯著，種間的基因流動對於種化機制的貢獻同樣不容小覷。本研究顯示菲律賓秋海棠組在地質、氣候與種間雜交的影響下形成盤根錯節的網狀親緣關係，為其演化歷史添加複雜性，也形塑菲律賓群島極高的生物多樣性。

Located at the fringing of the Eurasian plate and Philippine Sea plate, as well as the border of Asian biomes and Australian biomes, the Philippines is geographically and biogeographically the most complex area in Malesia featured with rich biodiversity resulted from intricate evolutionary histories. However, while the Philippines is regarded as the model island archipelago for evolutionary studies and many animal groups have been studied extensively, relatively few plant groups have been well sampled and investigated to understand what has triggered its high plant diversity. Begonia sect. Baryandra is a monophyletic group with ca. 90 species distributed almost entirely in the Philippines, representing an ideal study system to understand plant species radiation across the archipelago. Based on plastome sequences assembled using genome skimming approach and 1,238 nuclear genes obtained using target capture, highly resolved phylogenomic relationships of the groups were reconstructed. We also performed molecular dating and ancestral area reconstruction to infer the biogeographic history and used PhyloNetworks to investigate gene flows among species. Our results show that Sect. Baryandra colonized the Philippine archipelago first in Palawan, the westernmost island during the late Miocene via long-distance dispersal. Subsequently, plate tectonic movements and Pleistocene climatic fluctuations should have facilitated the expansion and migration of the section into adjacent islands. In addition to geologic and climatic factors, analyses of PhyloNetworks revealed homoploid hybrid speciation, chloroplast capture, and hybridization between multiple species all contributed to the cytonuclear incongruence, suggesting that reproductive barriers between species of the Sect. Baryandra have been weak and gene flow among species should have been crucial in generating high species diversity in the section. This study demonstrates that the complex geohistory of the Philippines, climatic fluctuation, and hybridization have all contributed to the intricate evolutionary history of Begonia sect. Baryandra, the complexity of which increases the difficulty of inferring its evolutionary histories and yet underscored the high biodiversity in the Philippines.